def write_nh_simspec_file(sim_name, sim_parms, sims_to_run, results_to_save,
output_dir):
'''Writes the Nano-Hive Sim specification file, which is an XML file that describes the
simulation environment, plugin selection and plugin parameters.
'''
# The Nano-Hive Sim Spec file has 4 different sections that must be written in the following order:
# 1. Header Section
# 2. Physical Interaction Plugin(s) Section
# 3. Results Plugin(s) Section
# 4. Footer Section.
# Mark 050915.
simspec_fname = get_nh_simspec_filename(sim_name)
workflow_fname = get_nh_workflow_filename(sim_name)
mmp_fname = get_nh_mmp_filename(sim_name)
f = open(simspec_fname, 'w') # Open Nano-Hive Sim Spec file.
sp = sim_parms
write_nh_header(f, sp.desc, sp.iterations, sp.spf, sp.temp, workflow_fname,
mmp_fname)
# Need to ask Brian about conditions for Bond record to be written.
if 0:
write_nh_bond_calc_rec(f)
# Physical Interaction Plugins ########################################
if "MPQC_ESP" in sims_to_run:
write_nh_mpqc_esp_plane_rec(f, sp.esp_image, output_dir)
if "MPQC_GD" in sims_to_run:
write_nh_mpqc_gd_rec(f)
if "AIREBO" in sims_to_run:
write_nh_airebo_rec(f)
# Results Plugins ########################################
if "MEASUREMENTS_TO_FILE" in results_to_save:
write_nh_measurements_to_file_results_rec(f, output_dir)
if "POVRAYVIDEO" in results_to_save:
write_nh_povrayvideo_results_rec(f, sim_name, output_dir)
if "NETCDF" in results_to_save:
write_nh_netcdf_results_rec(f, output_dir)
# Footer ########################################
write_nh_footer(f)
f.close()
def write_nh_simspec_file(sim_name, sim_parms, sims_to_run, results_to_save, output_dir):
"""
Writes the Nano-Hive Sim specification file, which is an XML file that describes the
simulation environment, plugin selection and plugin parameters.
"""
# The Nano-Hive Sim Spec file has 4 different sections that must be written in the following order:
# 1. Header Section
# 2. Physical Interaction Plugin(s) Section
# 3. Results Plugin(s) Section
# 4. Footer Section.
# Mark 050915.
simspec_fname = get_nh_simspec_filename(sim_name)
workflow_fname = get_nh_workflow_filename(sim_name)
mmp_fname = get_nh_mmp_filename(sim_name)
f = open(simspec_fname,'w') # Open Nano-Hive Sim Spec file.
sp = sim_parms
write_nh_header(f, sp.desc, sp.iterations, sp.spf, sp.temp, workflow_fname, mmp_fname)
# Need to ask Brian about conditions for Bond record to be written.
if 0:
write_nh_bond_calc_rec(f)
# Physical Interaction Plugins ########################################
if "MPQC_ESP" in sims_to_run:
write_nh_mpqc_esp_plane_rec(f, sp.esp_image, output_dir)
if "MPQC_GD" in sims_to_run:
write_nh_mpqc_gd_rec(f)
if "AIREBO" in sims_to_run:
write_nh_airebo_rec(f)
# Results Plugins ########################################
if "MEASUREMENTS_TO_FILE" in results_to_save:
write_nh_measurements_to_file_results_rec(f, output_dir)
if "POVRAYVIDEO" in results_to_save:
write_nh_povrayvideo_results_rec(f, sim_name, output_dir)
if "NETCDF" in results_to_save:
write_nh_netcdf_results_rec(f, output_dir)
# Footer ########################################
write_nh_footer(f)
f.close()
def write_nh_workflow_file(sim_name):
"""
Writes the Nano-Hive Workflow file, which is a TCL script used by Nano-Hive to
run the simulation. It describes the workflow of the simulation.
"""
workflow_fname = get_nh_workflow_filename(sim_name)
f = open(workflow_fname,'w')
f.write ('NH_Import $inFile\n\n')
f.write ('NH_Calculate 0 $traverser\n')
f.write ('NH_Calculate 0 $espImage $traverser\n')
f.write ('NH_Intermediate 0 $simResult\n\n')
f.write ('NH_Final $simResult\n')
f.close()
def write_nh_workflow_file(sim_name):
'''Writes the Nano-Hive Workflow file, which is a TCL script used by Nano-Hive to
run the simulation. It describes the workflow of the simulation.
'''
workflow_fname = get_nh_workflow_filename(sim_name)
f = open(workflow_fname, 'w')
f.write('NH_Import $inFile\n\n')
f.write('NH_Calculate 0 $traverser\n')
f.write('NH_Calculate 0 $espImage $traverser\n')
f.write('NH_Intermediate 0 $simResult\n\n')
f.write('NH_Final $simResult\n')
f.close()
